Heavy rains that began last Thursday have weakened and water levels were now subsiding, the Granma government mouthpiece said.
Four people have died in the eastern provinces of Granma, Las Tunas and Santiago de Cuba, while two perished in central Camaguey, it added.
Bridges, roads and sanitation systems were damaged by the rains, as well as several hundred homes.
Thousands of hectares of crops, including sugar cane, were destroyed in the island nation battling its worst economic crisis in decades.
"Undoubtedly, this was an atypical event," President Miguel Diaz-Canel said during a videoconference with provincial authorities late Monday, adding: "This has to do directly with climate change."
The president said flooding in some places reached levels not seen in 30 years, while residents of some areas reported levels never before seen.
The floods came after months of severe drought in Cuba's east.
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